Per chromosome imputation report for cohort ORPS_cohort.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 8.4.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 7206718 | 61.046 |
| 0.1 | 1217131 | 10.310 |
| 0.2 | 808714 | 6.850 |
| 0.3 | 618842 | 5.242 |
| 0.4 | 496324 | 4.204 |
| 0.5 | 408209 | 3.458 |
| 0.6 | 347234 | 2.941 |
| 0.7 | 293099 | 2.483 |
| 0.8 | 246053 | 2.084 |
| 0.9 | 163030 | 1.381 |
| Total | 11805354 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 320086 | 2.711 |
| 0.4 | 341848 | 2.896 |
| 0.5 | 430733 | 3.649 |
| 0.6 | 657402 | 5.569 |
| 0.7 | 1041614 | 8.823 |
| 0.8 | 1756496 | 14.879 |
| 0.9 | 7228707 | 61.232 |
| 1.0 | 28468 | 0.241 |
| Total | 11805354 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 547837 | 61.5314 |
| 0.1 | 89884 | 10.0955 |
| 0.2 | 57403 | 6.4473 |
| 0.3 | 45919 | 5.1575 |
| 0.4 | 37602 | 4.2233 |
| 0.5 | 30404 | 3.4149 |
| 0.6 | 27326 | 3.0692 |
| 0.7 | 21846 | 2.4537 |
| 0.8 | 18653 | 2.0950 |
| 0.9 | 13463 | 1.5121 |
| Total | 890337 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25264 | 2.8376 |
| 0.4 | 26183 | 2.9408 |
| 0.5 | 33281 | 3.7380 |
| 0.6 | 50587 | 5.6818 |
| 0.7 | 80200 | 9.0078 |
| 0.8 | 134554 | 15.1127 |
| 0.9 | 538310 | 60.4614 |
| 1.0 | 1958 | 0.2199 |
| Total | 890337 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 599164 | 61.5986 |
| 0.1 | 101638 | 10.4492 |
| 0.2 | 64623 | 6.6437 |
| 0.3 | 50351 | 5.1765 |
| 0.4 | 38241 | 3.9315 |
| 0.5 | 32123 | 3.3025 |
| 0.6 | 29074 | 2.9890 |
| 0.7 | 22786 | 2.3426 |
| 0.8 | 21149 | 2.1743 |
| 0.9 | 13542 | 1.3922 |
| Total | 972691 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25533 | 2.6250 |
| 0.4 | 27552 | 2.8326 |
| 0.5 | 33386 | 3.4323 |
| 0.6 | 50931 | 5.2361 |
| 0.7 | 82426 | 8.4740 |
| 0.8 | 141643 | 14.5620 |
| 0.9 | 608970 | 62.6067 |
| 1.0 | 2250 | 0.2313 |
| Total | 972691 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 503683 | 60.9231 |
| 0.1 | 87368 | 10.5676 |
| 0.2 | 56248 | 6.8035 |
| 0.3 | 42531 | 5.1443 |
| 0.4 | 34736 | 4.2015 |
| 0.5 | 29219 | 3.5342 |
| 0.6 | 24751 | 2.9938 |
| 0.7 | 20377 | 2.4647 |
| 0.8 | 16735 | 2.0242 |
| 0.9 | 11104 | 1.3431 |
| Total | 826752 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 21545 | 2.6060 |
| 0.4 | 22678 | 2.7430 |
| 0.5 | 28252 | 3.4172 |
| 0.6 | 43574 | 5.2705 |
| 0.7 | 70686 | 8.5498 |
| 0.8 | 119655 | 14.4729 |
| 0.9 | 518045 | 62.6603 |
| 1.0 | 2317 | 0.2803 |
| Total | 826752 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 500119 | 60.3195 |
| 0.1 | 81325 | 9.8086 |
| 0.2 | 60187 | 7.2592 |
| 0.3 | 45753 | 5.5183 |
| 0.4 | 33594 | 4.0518 |
| 0.5 | 27603 | 3.3292 |
| 0.6 | 24996 | 3.0148 |
| 0.7 | 21926 | 2.6445 |
| 0.8 | 19959 | 2.4073 |
| 0.9 | 13655 | 1.6469 |
| Total | 829117 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 20648 | 2.4904 |
| 0.4 | 22170 | 2.6739 |
| 0.5 | 27962 | 3.3725 |
| 0.6 | 42240 | 5.0946 |
| 0.7 | 69175 | 8.3432 |
| 0.8 | 119958 | 14.4682 |
| 0.9 | 525348 | 63.3623 |
| 1.0 | 1616 | 0.1949 |
| Total | 829117 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 466432 | 61.6097 |
| 0.1 | 76338 | 10.0833 |
| 0.2 | 52147 | 6.8880 |
| 0.3 | 40114 | 5.2986 |
| 0.4 | 31572 | 4.1703 |
| 0.5 | 24954 | 3.2961 |
| 0.6 | 22188 | 2.9308 |
| 0.7 | 18511 | 2.4451 |
| 0.8 | 15347 | 2.0271 |
| 0.9 | 9472 | 1.2511 |
| Total | 757075 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 19404 | 2.5630 |
| 0.4 | 20460 | 2.7025 |
| 0.5 | 25511 | 3.3697 |
| 0.6 | 39307 | 5.1920 |
| 0.7 | 63248 | 8.3543 |
| 0.8 | 108111 | 14.2801 |
| 0.9 | 478855 | 63.2507 |
| 1.0 | 2179 | 0.2878 |
| Total | 757075 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 455065 | 60.5524 |
| 0.1 | 79069 | 10.5212 |
| 0.2 | 52713 | 7.0142 |
| 0.3 | 40752 | 5.4226 |
| 0.4 | 32715 | 4.3532 |
| 0.5 | 26387 | 3.5111 |
| 0.6 | 21900 | 2.9141 |
| 0.7 | 17771 | 2.3647 |
| 0.8 | 15079 | 2.0065 |
| 0.9 | 10072 | 1.3402 |
| Total | 751523 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17815 | 2.3705 |
| 0.4 | 18604 | 2.4755 |
| 0.5 | 22926 | 3.0506 |
| 0.6 | 35135 | 4.6752 |
| 0.7 | 56156 | 7.4723 |
| 0.8 | 96860 | 12.8885 |
| 0.9 | 499269 | 66.4343 |
| 1.0 | 4758 | 0.6331 |
| Total | 751523 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 403103 | 60.6250 |
| 0.1 | 68447 | 10.2941 |
| 0.2 | 48425 | 7.2829 |
| 0.3 | 35172 | 5.2897 |
| 0.4 | 29620 | 4.4547 |
| 0.5 | 23629 | 3.5537 |
| 0.6 | 18868 | 2.8377 |
| 0.7 | 15855 | 2.3845 |
| 0.8 | 12604 | 1.8956 |
| 0.9 | 9189 | 1.3820 |
| Total | 664912 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17748 | 2.6692 |
| 0.4 | 18555 | 2.7906 |
| 0.5 | 23518 | 3.5370 |
| 0.6 | 36492 | 5.4882 |
| 0.7 | 58533 | 8.8031 |
| 0.8 | 98326 | 14.7878 |
| 0.9 | 410592 | 61.7513 |
| 1.0 | 1148 | 0.1727 |
| Total | 664912 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 395977 | 61.5020 |
| 0.1 | 64862 | 10.0742 |
| 0.2 | 44858 | 6.9672 |
| 0.3 | 31946 | 4.9618 |
| 0.4 | 27650 | 4.2945 |
| 0.5 | 22651 | 3.5181 |
| 0.6 | 18438 | 2.8637 |
| 0.7 | 15888 | 2.4677 |
| 0.8 | 13286 | 2.0635 |
| 0.9 | 8288 | 1.2873 |
| Total | 643844 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 16825 | 2.6132 |
| 0.4 | 18293 | 2.8412 |
| 0.5 | 22422 | 3.4825 |
| 0.6 | 33323 | 5.1756 |
| 0.7 | 54054 | 8.3955 |
| 0.8 | 91390 | 14.1944 |
| 0.9 | 405713 | 63.0142 |
| 1.0 | 1824 | 0.2833 |
| Total | 643844 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 307821 | 61.4686 |
| 0.1 | 55162 | 11.0153 |
| 0.2 | 32490 | 6.4879 |
| 0.3 | 25233 | 5.0388 |
| 0.4 | 20476 | 4.0888 |
| 0.5 | 16168 | 3.2286 |
| 0.6 | 14540 | 2.9035 |
| 0.7 | 11846 | 2.3655 |
| 0.8 | 9808 | 1.9586 |
| 0.9 | 7234 | 1.4446 |
| Total | 500778 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 13603 | 2.7164 |
| 0.4 | 14186 | 2.8328 |
| 0.5 | 17392 | 3.4730 |
| 0.6 | 27816 | 5.5546 |
| 0.7 | 45022 | 8.9904 |
| 0.8 | 75939 | 15.1642 |
| 0.9 | 306144 | 61.1337 |
| 1.0 | 676 | 0.1350 |
| Total | 500778 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 348871 | 60.6249 |
| 0.1 | 60089 | 10.4419 |
| 0.2 | 40187 | 6.9835 |
| 0.3 | 28434 | 4.9411 |
| 0.4 | 25344 | 4.4041 |
| 0.5 | 20777 | 3.6105 |
| 0.6 | 16672 | 2.8972 |
| 0.7 | 14263 | 2.4785 |
| 0.8 | 12776 | 2.2201 |
| 0.9 | 8045 | 1.3980 |
| Total | 575458 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14206 | 2.4686 |
| 0.4 | 15288 | 2.6567 |
| 0.5 | 19002 | 3.3021 |
| 0.6 | 28722 | 4.9912 |
| 0.7 | 47390 | 8.2352 |
| 0.8 | 84387 | 14.6643 |
| 0.9 | 365335 | 63.4860 |
| 1.0 | 1128 | 0.1960 |
| Total | 575458 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 351667 | 61.0488 |
| 0.1 | 57674 | 10.0121 |
| 0.2 | 36583 | 6.3508 |
| 0.3 | 31054 | 5.3909 |
| 0.4 | 24637 | 4.2769 |
| 0.5 | 20528 | 3.5636 |
| 0.6 | 18377 | 3.1902 |
| 0.7 | 14192 | 2.4637 |
| 0.8 | 12605 | 2.1882 |
| 0.9 | 8725 | 1.5146 |
| Total | 576042 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14253 | 2.4743 |
| 0.4 | 14474 | 2.5127 |
| 0.5 | 17910 | 3.1091 |
| 0.6 | 29248 | 5.0774 |
| 0.7 | 49485 | 8.5905 |
| 0.8 | 84042 | 14.5896 |
| 0.9 | 364855 | 63.3383 |
| 1.0 | 1775 | 0.3081 |
| Total | 576042 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 335334 | 61.1450 |
| 0.1 | 55734 | 10.1626 |
| 0.2 | 35697 | 6.5090 |
| 0.3 | 29802 | 5.4341 |
| 0.4 | 24022 | 4.3802 |
| 0.5 | 18940 | 3.4535 |
| 0.6 | 15692 | 2.8613 |
| 0.7 | 12677 | 2.3115 |
| 0.8 | 12796 | 2.3332 |
| 0.9 | 7730 | 1.4095 |
| Total | 548424 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14334 | 2.6137 |
| 0.4 | 15346 | 2.7982 |
| 0.5 | 19310 | 3.5210 |
| 0.6 | 29235 | 5.3307 |
| 0.7 | 47689 | 8.6956 |
| 0.8 | 81509 | 14.8624 |
| 0.9 | 339832 | 61.9652 |
| 1.0 | 1169 | 0.2132 |
| Total | 548424 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 252962 | 60.0539 |
| 0.1 | 42960 | 10.1988 |
| 0.2 | 28139 | 6.6803 |
| 0.3 | 22842 | 5.4228 |
| 0.4 | 17215 | 4.0869 |
| 0.5 | 15863 | 3.7659 |
| 0.6 | 12685 | 3.0115 |
| 0.7 | 11369 | 2.6990 |
| 0.8 | 9621 | 2.2841 |
| 0.9 | 7569 | 1.7969 |
| Total | 421225 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 10673 | 2.5338 |
| 0.4 | 11299 | 2.6824 |
| 0.5 | 13981 | 3.3191 |
| 0.6 | 21928 | 5.2058 |
| 0.7 | 36318 | 8.6220 |
| 0.8 | 60109 | 14.2700 |
| 0.9 | 265833 | 63.1095 |
| 1.0 | 1084 | 0.2573 |
| Total | 421225 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 225367 | 61.1672 |
| 0.1 | 39217 | 10.6440 |
| 0.2 | 25743 | 6.9870 |
| 0.3 | 18164 | 4.9299 |
| 0.4 | 15309 | 4.1550 |
| 0.5 | 11638 | 3.1587 |
| 0.6 | 9989 | 2.7111 |
| 0.7 | 9574 | 2.5985 |
| 0.8 | 7715 | 2.0939 |
| 0.9 | 5728 | 1.5546 |
| Total | 368444 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 9649 | 2.6189 |
| 0.4 | 10028 | 2.7217 |
| 0.5 | 12792 | 3.4719 |
| 0.6 | 19932 | 5.4098 |
| 0.7 | 31321 | 8.5009 |
| 0.8 | 53774 | 14.5949 |
| 0.9 | 230275 | 62.4993 |
| 1.0 | 673 | 0.1827 |
| Total | 368444 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 200536 | 61.3267 |
| 0.1 | 32287 | 9.8738 |
| 0.2 | 22715 | 6.9466 |
| 0.3 | 17283 | 5.2854 |
| 0.4 | 13679 | 4.1832 |
| 0.5 | 11868 | 3.6294 |
| 0.6 | 8876 | 2.7144 |
| 0.7 | 7832 | 2.3951 |
| 0.8 | 6801 | 2.0798 |
| 0.9 | 5119 | 1.5655 |
| Total | 326996 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 9748 | 2.9811 |
| 0.4 | 10930 | 3.3425 |
| 0.5 | 13990 | 4.2783 |
| 0.6 | 20558 | 6.2869 |
| 0.7 | 30945 | 9.4634 |
| 0.8 | 51359 | 15.7063 |
| 0.9 | 188979 | 57.7925 |
| 1.0 | 487 | 0.1489 |
| Total | 326996 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 219924 | 61.7102 |
| 0.1 | 37323 | 10.4728 |
| 0.2 | 22876 | 6.4190 |
| 0.3 | 18917 | 5.3081 |
| 0.4 | 14271 | 4.0044 |
| 0.5 | 12389 | 3.4763 |
| 0.6 | 10624 | 2.9811 |
| 0.7 | 9421 | 2.6435 |
| 0.8 | 6692 | 1.8778 |
| 0.9 | 3945 | 1.1070 |
| Total | 356382 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 10183 | 2.8573 |
| 0.4 | 11339 | 3.1817 |
| 0.5 | 14191 | 3.9820 |
| 0.6 | 23118 | 6.4869 |
| 0.7 | 36692 | 10.2957 |
| 0.8 | 61907 | 17.3710 |
| 0.9 | 198615 | 55.7309 |
| 1.0 | 337 | 0.0946 |
| Total | 356382 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 186900 | 61.0365 |
| 0.1 | 30484 | 9.9553 |
| 0.2 | 22900 | 7.4785 |
| 0.3 | 15798 | 5.1592 |
| 0.4 | 12995 | 4.2438 |
| 0.5 | 11413 | 3.7272 |
| 0.6 | 8981 | 2.9330 |
| 0.7 | 8024 | 2.6204 |
| 0.8 | 5784 | 1.8889 |
| 0.9 | 2931 | 0.9572 |
| Total | 306210 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 10154 | 3.3160 |
| 0.4 | 11530 | 3.7654 |
| 0.5 | 15390 | 5.0260 |
| 0.6 | 22059 | 7.2039 |
| 0.7 | 33038 | 10.7893 |
| 0.8 | 51731 | 16.8940 |
| 0.9 | 161909 | 52.8752 |
| 1.0 | 399 | 0.1303 |
| Total | 306210 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 197665 | 60.4216 |
| 0.1 | 34186 | 10.4499 |
| 0.2 | 23588 | 7.2103 |
| 0.3 | 17549 | 5.3643 |
| 0.4 | 13970 | 4.2703 |
| 0.5 | 11147 | 3.4074 |
| 0.6 | 8972 | 2.7425 |
| 0.7 | 8474 | 2.5903 |
| 0.8 | 6775 | 2.0710 |
| 0.9 | 4817 | 1.4724 |
| Total | 327143 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 9570 | 2.9253 |
| 0.4 | 9761 | 2.9837 |
| 0.5 | 13373 | 4.0878 |
| 0.6 | 20192 | 6.1722 |
| 0.7 | 30612 | 9.3574 |
| 0.8 | 51902 | 15.8652 |
| 0.9 | 191291 | 58.4732 |
| 1.0 | 442 | 0.1351 |
| Total | 327143 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 152489 | 60.3838 |
| 0.1 | 29173 | 11.5522 |
| 0.2 | 19004 | 7.5254 |
| 0.3 | 13012 | 5.1526 |
| 0.4 | 9658 | 3.8245 |
| 0.5 | 8987 | 3.5587 |
| 0.6 | 6983 | 2.7652 |
| 0.7 | 5992 | 2.3728 |
| 0.8 | 4643 | 1.8386 |
| 0.9 | 2592 | 1.0264 |
| Total | 252533 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 7931 | 3.1406 |
| 0.4 | 9298 | 3.6819 |
| 0.5 | 12534 | 4.9633 |
| 0.6 | 18814 | 7.4501 |
| 0.7 | 27945 | 11.0659 |
| 0.8 | 43966 | 17.4100 |
| 0.9 | 131590 | 52.1080 |
| 1.0 | 455 | 0.1802 |
| Total | 252533 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 158876 | 61.4180 |
| 0.1 | 27377 | 10.5833 |
| 0.2 | 17763 | 6.8668 |
| 0.3 | 13661 | 5.2810 |
| 0.4 | 11044 | 4.2694 |
| 0.5 | 8826 | 3.4119 |
| 0.6 | 7642 | 2.9542 |
| 0.7 | 5930 | 2.2924 |
| 0.8 | 4665 | 1.8034 |
| 0.9 | 2896 | 1.1195 |
| Total | 258680 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 7357 | 2.8441 |
| 0.4 | 7701 | 2.9770 |
| 0.5 | 10542 | 4.0753 |
| 0.6 | 16387 | 6.3349 |
| 0.7 | 25260 | 9.7650 |
| 0.8 | 41643 | 16.0983 |
| 0.9 | 149500 | 57.7934 |
| 1.0 | 290 | 0.1121 |
| Total | 258680 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 90188 | 58.7379 |
| 0.1 | 15932 | 10.3762 |
| 0.2 | 10516 | 6.8489 |
| 0.3 | 8531 | 5.5561 |
| 0.4 | 7459 | 4.8579 |
| 0.5 | 5994 | 3.9038 |
| 0.6 | 4940 | 3.2173 |
| 0.7 | 4635 | 3.0187 |
| 0.8 | 3885 | 2.5302 |
| 0.9 | 1463 | 0.9528 |
| Total | 153543 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 4467 | 2.9093 |
| 0.4 | 4603 | 2.9979 |
| 0.5 | 6457 | 4.2053 |
| 0.6 | 9976 | 6.4972 |
| 0.7 | 14883 | 9.6931 |
| 0.8 | 24889 | 16.2098 |
| 0.9 | 88082 | 57.3663 |
| 1.0 | 186 | 0.1211 |
| Total | 153543 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 91661 | 60.7686 |
| 0.1 | 15806 | 10.4789 |
| 0.2 | 10904 | 7.2290 |
| 0.3 | 8186 | 5.4271 |
| 0.4 | 6624 | 4.3915 |
| 0.5 | 5318 | 3.5257 |
| 0.6 | 4527 | 3.0013 |
| 0.7 | 3881 | 2.5730 |
| 0.8 | 2618 | 1.7357 |
| 0.9 | 1311 | 0.8692 |
| Total | 150836 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 5029 | 3.3341 |
| 0.4 | 5451 | 3.6139 |
| 0.5 | 6853 | 4.5433 |
| 0.6 | 11016 | 7.3033 |
| 0.7 | 15837 | 10.4995 |
| 0.8 | 25721 | 17.0523 |
| 0.9 | 80781 | 53.5555 |
| 1.0 | 148 | 0.0981 |
| Total | 150836 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 215077 | 62.0876 |
| 0.1 | 34796 | 10.0448 |
| 0.2 | 23005 | 6.6410 |
| 0.3 | 17838 | 5.1494 |
| 0.4 | 13891 | 4.0100 |
| 0.5 | 11383 | 3.2860 |
| 0.6 | 10193 | 2.9425 |
| 0.7 | 10029 | 2.8951 |
| 0.8 | 6057 | 1.7485 |
| 0.9 | 4140 | 1.1951 |
| Total | 346409 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14147 | 4.0839 |
| 0.4 | 16119 | 4.6532 |
| 0.5 | 19758 | 5.7037 |
| 0.6 | 26812 | 7.7400 |
| 0.7 | 34699 | 10.0168 |
| 0.8 | 53121 | 15.3348 |
| 0.9 | 180584 | 52.1303 |
| 1.0 | 1169 | 0.3375 |
| Total | 346409 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering